Filter single cells by a specific gene in scRNAseq dataset using scanpy


I am processing scRNAseq data using scanpy on Galaxy. Is there a way to filter cells specifically on a single gene. e.g. if I wanted to filter my cells to include only those cells that express gene “X” at counts of 3 or more for instance.



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Hi @joshua.harvey.20

Yes, but I’m pretty sure that will need to annotate the cells before you can query based on that annotation (and other attributes).

These are our single-cell tutorials. You can also search the site with tool names, like “scanpy”.